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Doc build errors #41

Description

@jimc101

Describe the bug
There are lots of warnings reported as the docs are built, although the docs do still build. These include cookbooks missing from toctrees, problems with section headers, issues with nml files etc.

To Reproduce
1 Clone the PyFVCOM2 repo
2 Install the PyFVCOM2 package and docs dependencies
3 Build the docs by typing:

$ make html

Expected behavior
Docs build without error.

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Additional context
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